You kinda' contradicted yourself there. You said New Vegas was so linear, but then mentioned that you "could join the Legion." That's a key detail there; you can join the Legion. Or the NCR. Or House. Or you can [censored] 'em all. That's more choice than Fallout 3 ever had, where no matter what, you
had to join the Brotherhood of Steel and fight the Enclave, no ifs, ands, or buts.
As for story, well it takes all kinds, but I much prefer NV's. It's politically-charged, the moral spectrum is gray all around as opposed to the black-and-white morality of FO3, it's not just a loose rehash of the previous games' plots, and the world design actually makes sense. To say nothing of the dialogue and characters, all of which are better written and multifaceted.
Weapons are much better too. There's a lot more of them around, and though there's a definite progression in the various types, it's not very linear at all. For example, the weapons build for sniping, like the hunting rifle, sniper rifle, and AMR all have various advantages and disadvantages over each other.
Leveling's been improved as well. The perks are far more interesting (not one skill booster among them), and the limit to one every two levels gives them added weight and helps make for more varied character builds and playstyles.
As for bug-ridden, I don't know what you're talking about. People still harp on the bugs that were out on release, but a lot of them got fixed a long time ago. It's really no worse than FO3, which also has its share of annoying bugs that Bethesda never bothered to patch.